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- PDB-2e3w: X-ray structure of native RNase A -

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Basic information

Entry
Database: PDB / ID: 2e3w
TitleX-ray structure of native RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / alpha-helix / beta-sheet
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBoerema, D.J. / Tereshko, V.A. / Kent, S.B.H.
CitationJournal: Biopolymers / Year: 2008
Title: Total synthesis by modern chemical ligation methods and high resolution (1.1 A) X-ray structure of ribonuclease A
Authors: Boerema, D.J. / Tereshko, V.A. / Kent, S.B.
History
DepositionNov 30, 2006Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8154
Polymers13,7081
Non-polymers1063
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.167, 64.167, 63.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.89
Details: Well solution: Combination of Hampton Index Reagents 3 and 9, Final solution: 0.1 M Bis-tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop: 2 microliter well solution + 2 microliter 10 ...Details: Well solution: Combination of Hampton Index Reagents 3 and 9, Final solution: 0.1 M Bis-tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop: 2 microliter well solution + 2 microliter 10 mg/ml protein solution in water, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9002 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 69871

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IZP

1izp


Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.656 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20783 3523 5 %RANDOM
Rwork0.1925 ---
obs0.19329 66348 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.424 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å20 Å2
2---0.33 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 3 182 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211006
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9221367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46525.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86915176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.959154
X-RAY DIFFRACTIONr_chiral_restr0.1060.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02763
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2707
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8041.5649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50721043
X-RAY DIFFRACTIONr_scbond_it2.7193392
X-RAY DIFFRACTIONr_scangle_it3.534.5324
X-RAY DIFFRACTIONr_rigid_bond_restr1.8333737
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded6.7853702
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 236 -
Rwork0.241 4738 -
obs--96.36 %

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